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Beatrice Tan
CNAprioritization
Commits
42ec6850
Commit
42ec6850
authored
Feb 05, 2018
by
BeatriceTan
Browse files
Updated GO enrichment analysis to save plot.
parent
c246d616
Changes
6
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Snakefile
View file @
42ec6850
...
...
@@ -17,7 +17,7 @@ include: "rules/ComparisonRegions.smk"
include: "rules/Circos.smk"
include: "rules/SampleSizes.smk"
include: "rules/UseControl.smk"
include: "rules/ComparisonSettings.smk"
#
include: "rules/ComparisonSettings.smk"
#Directory to save all files.
workdir: config["workdir"]
...
...
@@ -43,10 +43,10 @@ onerror:
rule all:
"""Define desired output from pipeline."""
input:
"GO/comparison.txt",
"Settings/Report.txt",
#"Samplesize/Report.txt",
#"Reports/Tools.txt",
"GO/comparison.txt",
#"Settings/Report.txt",
#"Samplesize/Report.txt",aomt
#"Samplesize/Report.txt"
rule help:
...
...
config.yaml
View file @
42ec6850
...
...
@@ -21,7 +21,7 @@ biomart_genes: input_files/biomart_human_genes.tsv
ID_to_GO
:
input_files/ID_to_GO.txt
#Settings GISTIC2.0
gistic_precision
:
"
99
"
gistic_precision
:
"
75
"
settings_gistic
:
"
-ta
0.1
-td
0.1
-qvt
0.25
...
...
@@ -29,7 +29,7 @@ settings_gistic: "-ta 0.1
-cap
1.5
-rx
1
-genegistic
1
-conf
0.
99
"
-conf
0.
75
"
comparison_settings
:
[
"
-ta
0.1
-td
0.1
-qvt
0.25
-brlen
0.7
-cap
1.5
-rx
1
-genegistic
1
-conf
0.99"
,
"
-ta
0.1
-td
0.1
-qvt
0.25
-brlen
0.7
-cap
1.5
-rx
1
-genegistic
1
-conf
0.75"
,
...
...
rules/ComparisonSettings.smk
View file @
42ec6850
...
...
@@ -7,12 +7,12 @@ rule gistic_settings:
seg="Input/Segments_tumor.txt"
output:
expand("Settings/GISTIC_{setting_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", setting_nr=range(len(config["comparison_settings"]))),
expand(
"Settings/GISTIC_{setting_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed"
, setting_nr=range(len(config["comparison_settings"])))
"Settings/GISTIC_{setting_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed"
params:
cnv="",
ref=config["reference"],
ref_file="",
extra=
expand("{setting}", setting=
config["comparison_settings"])
extra=
(
config["comparison_settings"])
[int("{setting_nr}")]
wrapper:
"file:" + workflow.basedir + "/wrappers/GISTIC2"
...
...
rules/GenePrioritization.smk
View file @
42ec6850
...
...
@@ -3,7 +3,8 @@ rule go_analysis:
input:
gene_list="Reports/Genes_{tool}.txt"
output:
go="GO/{tool}.txt"
table="GO/Enriched_GOs_{tool}.txt",
plot="GO/Enriched_GOs_{tool}.jpg"
params:
organism="hsapiens", #default is human
ontology="BP", #MF, BP, CC or all
...
...
@@ -16,7 +17,7 @@ rule go_analysis:
rule compare_enriched_terms:
"""Compare the top 50 GO terms detected by RUBIC and GISTIC2.0"""
input:
go=expand("GO/{tool}.txt", tool=["GISTIC2", "RUBIC"])
go=expand("GO/
Enriched_GOs_
{tool}.txt", tool=["GISTIC2", "RUBIC"])
output:
"GO/comparison.txt"
run:
...
...
scripts/ReportTools.py
View file @
42ec6850
...
...
@@ -104,12 +104,13 @@ def venn3_overlap(gene_lists, known_genes, out_venn):
def
plot_histogram_sizes
(
parsed_results
,
plot_file
):
"""Make boxplot with swarmplot on top showing sizes of recurrent regions detected by GISTIC2.0 and RUBIC."""
size_list
,
size_list_known
=
parse_sizes_for_plot
(
parsed_results
)
print
(
size_list_known
)
sns
.
set_style
(
"white"
)
f
,
ax
=
plt
.
subplots
(
figsize
=
(
7
,
7
))
ax
.
set
(
yscale
=
"log"
)
g
=
sns
.
boxplot
(
x
=
"Tool"
,
y
=
"Size"
,
hue
=
"CNV type"
,
data
=
size_list
,
whis
=
np
.
inf
,
palette
=
{
"Amplification"
:
"#71AEC0"
,
"Deletion"
:
"#B55D60"
})
g
=
sns
.
swarmplot
(
x
=
"Tool"
,
y
=
"Size"
,
dodge
=
True
,
hue
=
"CNV type"
,
data
=
size_list
,
size
=
5
,
palette
=
{
"Amplification"
:
"#527F8C"
,
"Deletion"
:
"#844446"
})
g
=
sns
.
swarmplot
(
x
=
"Tool"
,
y
=
"Size"
,
dodge
=
True
,
hue
=
"CNV type"
,
data
=
size_list_known
,
size
=
5
,
palette
=
{
"Amplification"
:
"black"
,
"Deletion"
:
"black"
})
#
g = sns.swarmplot(x="Tool", y="Size", dodge=True, hue="CNV type", data=size_list_known, size=5, palette={"Amplification": "black", "Deletion": "black"})
sns
.
despine
()
g
.
set_xlabel
(
"Tool"
,
fontsize
=
16
)
g
.
set_ylabel
(
"Log size of recurrent regions"
,
fontsize
=
16
)
...
...
wrappers/topgo/wrapper.R
View file @
42ec6850
...
...
@@ -48,5 +48,7 @@ print(allRes)
write.table
(
allRes
,
file
=
snakemake
@
output
[[
1
]],
quote
=
FALSE
,
sep
=
"\t"
,
eol
=
"\n"
)
#Visualize GO term relationships
jpeg
(
snakemake
@
output
[[
1
]])
showSigOfNodes
(
GOdata
,
score
(
resultFisher
),
firstSigNodes
=
5
,
useInfo
=
'all'
)
printGraph
(
GOdata
,
resultFisher
,
firstSigNodes
=
5
,
fn.prefix
=
"tGO"
,
useInfo
=
"all"
,
pdfSW
=
TRUE
)
dev.off
()
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